Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
end
def index
+ @objects = nil if !defined?(@objects)
find_objects_for_index if !@objects
render_index
end
end
def choose
+ @objects = nil if !defined?(@objects)
params[:limit] ||= 40
respond_to do |f|
if params[:partial]
def accept_uuid_as_id_param
- if params[:id] and params[:id].match /\D/
+ if params[:id] and params[:id].match(/\D/)
params[:uuid] = params.delete :id
end
end
helper_method :user_notifications
def user_notifications
+ @errors = nil if !defined?(@errors)
return [] if @errors or not current_user.andand.is_active or not Rails.configuration.show_user_notifications
@notifications ||= @@notification_tests.map do |t|
t.call(self, current_user)
helper_method :my_starred_projects
def my_starred_projects user
- return if @starred_projects
+ return if defined?(@starred_projects) && @starred_projects
links = Link.filter([['tail_uuid', '=', user.uuid],
['link_class', '=', 'star'],
['head_uuid', 'is_a', 'arvados#group']]).select(%w(head_uuid))
# That is: get toplevel projects under home, get subprojects of
# these projects, and so on until we hit the limit.
def my_wanted_projects(user, page_size=100)
- return @my_wanted_projects if @my_wanted_projects
+ return @my_wanted_projects if defined?(@my_wanted_projects) && @my_wanted_projects
from_top = []
uuids = [user.uuid]
end
def build_my_wanted_projects_tree(user, page_size=100)
- return @my_wanted_projects_tree if @my_wanted_projects_tree
+ return @my_wanted_projects_tree if defined?(@my_wanted_projects_tree) && @my_wanted_projects_tree
parent_of = {user.uuid => 'me'}
my_wanted_projects(user, page_size).each do |ob|
children_of[parent_of[ob.uuid]] ||= []
children_of[parent_of[ob.uuid]] << ob
end
- buildtree = lambda do |children_of, root_uuid=false|
+ buildtree = lambda do |chldrn_of, root_uuid=false|
tree = {}
- children_of[root_uuid].andand.each do |ob|
- tree[ob] = buildtree.call(children_of, ob.uuid)
+ chldrn_of[root_uuid].andand.each do |ob|
+ tree[ob] = buildtree.call(chldrn_of, ob.uuid)
end
tree
end
def remove_items
@removed_uuids = []
- links = []
params[:item_uuids].collect { |uuid| ArvadosBase.find uuid }.each do |item|
if item.class == Collection or item.class == Group
# Use delete API on collections and projects/groups
end
def current_api_host
- Rails.configuration.arvados_v1_base.gsub /https?:\/\/|\/arvados\/v1/,''
+ Rails.configuration.arvados_v1_base.gsub(/https?:\/\/|\/arvados\/v1/, '')
end
def current_uuid_prefix
def cwl_inputs_required(object, inputs_schema, set_attr_path)
r = 0
inputs_schema.each do |input|
- required, primary_type, param_id = cwl_input_info(input)
- dn, attrvalue = cwl_input_value(object, input, set_attr_path + [param_id])
+ required, _, param_id = cwl_input_info(input)
+ _, attrvalue = cwl_input_value(object, input, set_attr_path + [param_id])
r += 1 if required and attrvalue.nil?
end
r
private
def is_textile?( object, attr )
- is_textile = object.textile_attributes.andand.include?(attr)
+ object.textile_attributes.andand.include?(attr)
end
end
# For the benefit of themes that still expect $arvados_api_client to work:
class ArvadosClientProxyHack
def method_missing *args
- ArvadosApiClient.new_or_current.send *args
+ ArvadosApiClient.new_or_current.send(*args)
end
end
$arvados_api_client = ArvadosClientProxyHack.new
f0 = '' if f0 == '.'
f0 = f0[2..-1] if f0[0..1] == './'
f0 += '/' if not f0.empty?
- file_path = "#{f0}#{file[1]}"
+ "#{f0}#{file[1]}"
end
##
end
else
if step[:progress] and
- (re = step[:progress].match /^(\d+)\+(\d+)\/(\d+)$/)
+ (re = step[:progress].match(/^(\d+)\+(\d+)\/(\d+)$/))
pj[:progress] = (((re[1].to_f + re[2].to_f/2) / re[3].to_f) rescue 0.5)
else
pj[:progress] = 0.0
{label: 'output'})
end
# Input collection nodes
- output_pdhs = @opts[:output_collections].values.collect{|c|
- c[:portable_data_hash]}
+ output_pdhs = @opts[:output_collections].values.collect{|oc|
+ oc[:portable_data_hash]}
ProvenanceHelper::cr_input_pdhs(cr).each do |pdh|
if not output_pdhs.include?(pdh)
# Search for collections on the same project first
- cols = @opts[:input_collections][pdh].andand.select{|c|
- c[:owner_uuid] == cr[:owner_uuid]}
+ cols = @opts[:input_collections][pdh].andand.select{|ic|
+ ic[:owner_uuid] == cr[:owner_uuid]}
if not cols or cols.empty?
# Search for any collection with this PDH
cols = @opts[:input_collections][pdh]
end
def self.columns
+ @discovered_columns = [] if !defined?(@discovered_columns)
return @discovered_columns if @discovered_columns.andand.any?
- @discovered_columns = []
@attribute_info ||= {}
schema = arvados_api_client.discovery[:schemas][self.to_s.to_sym]
return @discovered_columns if schema.nil?
if opts[:class].is_a? Class
return opts[:class]
end
- if uuid.match /^[0-9a-f]{32}(\+[^,]+)*(,[0-9a-f]{32}(\+[^,]+)*)*$/
+ if uuid.match(/^[0-9a-f]{32}(\+[^,]+)*(,[0-9a-f]{32}(\+[^,]+)*)*$/)
return Collection
end
resource_class = nil
- uuid.match /^[0-9a-z]{5}-([0-9a-z]{5})-[0-9a-z]{15}$/ do |re|
+ uuid.match(/^[0-9a-z]{5}-([0-9a-z]{5})-[0-9a-z]{15}$/) do |re|
resource_class ||= arvados_api_client.
kind_class(self.uuid_infix_object_kind[re[1]])
end
if opts[:referring_object] and
opts[:referring_attr] and
- opts[:referring_attr].match /_uuid$/
+ opts[:referring_attr].match(/_uuid$/)
resource_class ||= arvados_api_client.
kind_class(opts[:referring_object].
attributes[opts[:referring_attr].
@fetch_multiple_pages = true
@arvados_api_token = Thread.current[:arvados_api_token]
@reader_tokens = Thread.current[:reader_tokens]
+ @results = nil
+ @count = nil
+ @offset = 0
+ @cond = nil
+ @eager = nil
+ @select = nil
+ @orderby_spec = nil
+ @filters = nil
+ @distinct = nil
+ @include_trash = nil
+ @limit = nil
end
def eager(bool=true)
end
end
end
- @cond.keys.select { |x| x.match /_kind$/ }.each do |kind_key|
+ @cond.keys.select { |x| x.match(/_kind$/) }.each do |kind_key|
if @cond[kind_key].is_a? Class
@cond = @cond.merge({ kind_key => 'arvados#' + arvados_api_client.class_kind(@cond[kind_key]) })
end
def each(&block)
if not @results.nil?
- @results.each &block
+ @results.each(&block)
else
self.each_page do |items|
items.each do |i|
arvados_api_client.api "collections/#{self.uuid}/", "used_by"
end
- def uuid
- if self[:uuid].nil?
- return self[:portable_data_hash]
- else
- super
- end
- end
-
def friendly_link_name lookup=nil
name || portable_data_hash
end
@container = Container.find(container_uuid)
end
end
+ @container = nil if !defined?(@container)
@child_proxies = child_objects
end
} %>
</ul>
</li>
- <% if @name_link or @object %>
+ <% if (defined?(@name_link) && @name_link) or (defined?(@object) && @object) %>
<li class="nav-separator">
<i class="fa fa-lg fa-angle-double-right"></i>
</li>
<meta property="og:type" content="article" />
<meta property="og:url" content="<%= request.url %>" />
<meta property="og:site_name" content="<%= Rails.configuration.site_name %>" />
- <% if @object %>
+ <% if defined?(@object) && @object %>
<% if @object.respond_to?(:name) and @object.name.present? %>
<meta property="og:title" content="<%= @object.name%>" />
<% end %>
recent_cr_containers = recent_crs.map {|cr| cr.container_uuid}.compact.uniq
preload_objects_for_dataclass(Container, recent_cr_containers) if recent_cr_containers.andand.any?
- # fetch children of all the active crs in one call, if there are any
- active_crs = recent_crs.each {|cr| cr if (cr.priority.andand > 0 and cr.state != 'Final' and cr.container_uuid)}
-
wus = {}
outputs = []
recent_procs.each do |p|
# end
ActiveSupport::Inflector.inflections do |inflect|
- inflect.plural /^([Ss]pecimen)$/i, '\1s'
- inflect.singular /^([Ss]pecimen)s?/i, '\1'
- inflect.plural /^([Hh]uman)$/i, '\1s'
- inflect.singular /^([Hh]uman)s?/i, '\1'
+ inflect.plural(/^([Ss]pecimen)$/i, '\1s')
+ inflect.singular(/^([Ss]pecimen)s?/i, '\1')
+ inflect.plural(/^([Hh]uman)$/i, '\1s')
+ inflect.singular(/^([Hh]uman)s?/i, '\1')
end
%w(application.default application).each do |cfgfile|
path = "#{::Rails.root.to_s}/config/#{cfgfile}.yml"
- if File.exists? path
+ if File.exist? path
yaml = ERB.new(IO.read path).result(binding)
confs = YAML.load(yaml, deserialize_symbols: true)
$application_config.merge!(confs['common'] || {})
# exception if not found. Use this with assertions to explain that
# the error signifies a failed test rather than an unexpected error
# during a testing procedure.
- def find? *args
+ def find?(*args)
begin
- find *args
+ find(*args)
rescue Capybara::ElementNotFound
false
end
def after_teardown
if self.class.want_reset_api_fixtures[:after_each_test] and
- @want_reset_api_fixtures != false
+ (!defined?(@want_reset_api_fixtures) or @want_reset_api_fixtures != false)
self.class.reset_api_fixtures_now
end
super
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
- /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
/usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
# Install golang binary
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
- /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
/usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
# Install golang binary
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
- /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
/usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
# Install golang binary
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
- /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
/usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
# Install golang binary
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
- /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
/usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
# Install golang binary
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
RUN gpg --import --no-tty /tmp/mpapis.asc && \
gpg --import --no-tty /tmp/pkuczynski.asc && \
curl -L https://get.rvm.io | bash -s stable && \
- /usr/local/rvm/bin/rvm install 2.3 && \
- /usr/local/rvm/bin/rvm alias create default ruby-2.3
+ /usr/local/rvm/bin/rvm install 2.5 && \
+ /usr/local/rvm/bin/rvm alias create default ruby-2.5
# udev daemon can't start in a container, so don't try.
RUN mkdir -p /etc/udev/disabled
&& cd "$WORKSPACE/$srcpath" \
&& bundle_install_trylocal \
&& gem build "$gemname.gemspec" \
- && with_test_gemset gem install --no-ri --no-rdoc $(ls -t "$gemname"-*.gem|head -n1)
+ && with_test_gemset gem install --no-document $(ls -t "$gemname"-*.gem|head -n1)
}
install_sdk/ruby() {
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-Ruby 2.3 is recommended; Ruby 2.1 is also known to work.
+Ruby 2.5 is recommended; Ruby 2.3 is also known to work.
h4(#rvm). *Option 1: Install with RVM*
<notextile>
-<pre><code><span class="userinput">sudo gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
-\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.3
+<pre><code><span class="userinput">sudo gpg --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
+\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.5
</span></code></pre></notextile>
Either log out and log back in to activate RVM, or explicitly load it in all open shells like this:
<notextile>
<pre><code><span class="userinput">mkdir -p ~/src
cd ~/src
-curl -f http://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.3.tar.gz | tar xz
-cd ruby-2.3.3
+curl -f http://cache.ruby-lang.org/pub/ruby/2.5/ruby-2.5.5.tar.gz | tar xz
+cd ruby-2.5.5
./configure --disable-install-rdoc
make
sudo make install
--- /dev/null
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Ruby 2.3 is recommended; Ruby 2.1 is also known to work.
+
+h4(#rvm). *Option 1: Install with RVM*
+
+<notextile>
+<pre><code><span class="userinput">sudo gpg --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
+\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.3
+</span></code></pre></notextile>
+
+Either log out and log back in to activate RVM, or explicitly load it in all open shells like this:
+
+<notextile>
+<pre><code><span class="userinput">source /usr/local/rvm/scripts/rvm
+</span></code></pre></notextile>
+
+Once RVM is activated in your shell, install Bundler:
+
+<notextile>
+<pre><code>~$ <span class="userinput">gem install bundler</span>
+</code></pre></notextile>
+
+h4(#fromsource). *Option 2: Install from source*
+
+Install prerequisites for Debian 8:
+
+<notextile>
+<pre><code><span class="userinput">sudo apt-get install \
+ bison build-essential gettext libcurl3 libcurl3-gnutls \
+ libcurl4-openssl-dev libpcre3-dev libreadline-dev \
+ libssl-dev libxslt1.1 zlib1g-dev
+</span></code></pre></notextile>
+
+Install prerequisites for CentOS 7:
+
+<notextile>
+<pre><code><span class="userinput">sudo yum install \
+ libyaml-devel glibc-headers autoconf gcc-c++ glibc-devel \
+ patch readline-devel zlib-devel libffi-devel openssl-devel \
+ make automake libtool bison sqlite-devel tar
+</span></code></pre></notextile>
+
+Install prerequisites for Ubuntu 12.04 or 14.04:
+
+<notextile>
+<pre><code><span class="userinput">sudo apt-get install \
+ gawk g++ gcc make libc6-dev libreadline6-dev zlib1g-dev libssl-dev \
+ libyaml-dev libsqlite3-dev sqlite3 autoconf libgdbm-dev \
+ libncurses5-dev automake libtool bison pkg-config libffi-dev curl
+</span></code></pre></notextile>
+
+Build and install Ruby:
+
+<notextile>
+<pre><code><span class="userinput">mkdir -p ~/src
+cd ~/src
+curl -f http://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.3.tar.gz | tar xz
+cd ruby-2.3.3
+./configure --disable-install-rdoc
+make
+sudo make install
+
+sudo -i gem install bundler</span>
+</code></pre></notextile>
h3(#install_ruby_and_bundler). Install Ruby and Bundler
-{% include 'install_ruby_and_bundler' %}
+{% include 'install_ruby_and_bundler_sso' %}
h3(#install_web_server). Set up a Web server
uglifier (~> 2.0)
BUNDLED WITH
- 1.16.6
+ 1.17.3
conditions[0] << " and #{ar_table_name}.#{attr} in (?)"
conditions << value
end
- elsif value.is_a? String or value.is_a? Fixnum or value == true or value == false
+ elsif value.is_a? String or value.is_a? Integer or value == true or value == false
conditions[0] << " and #{ar_table_name}.#{attr}=?"
conditions << value
elsif value.is_a? Hash
begin
must_git gitdir, "branch"
rescue GitError => e
- raise unless /Not a git repository/ =~ e.to_s
+ raise unless /Not a git repository/i =~ e.to_s
# OK, this just means we need to create a blank cache repository
# before fetching.
FileUtils.mkdir_p gitdir
--- /dev/null
+PATH
+ remote: .
+ specs:
+ arvados-login-sync (1.3.3.20190528194843)
+ arvados (~> 1.3.0, >= 1.3.0)
+
+GEM
+ remote: https://rubygems.org/
+ specs:
+ activesupport (5.0.7.2)
+ concurrent-ruby (~> 1.0, >= 1.0.2)
+ i18n (>= 0.7, < 2)
+ minitest (~> 5.1)
+ tzinfo (~> 1.1)
+ addressable (2.6.0)
+ public_suffix (>= 2.0.2, < 4.0)
+ andand (1.3.3)
+ arvados (1.3.3.20190320201707)
+ activesupport (>= 3)
+ andand (~> 1.3, >= 1.3.3)
+ arvados-google-api-client (>= 0.7, < 0.8.9)
+ i18n (~> 0)
+ json (>= 1.7.7, < 3)
+ jwt (>= 0.1.5, < 2)
+ arvados-google-api-client (0.8.7.2)
+ activesupport (>= 3.2, < 5.1)
+ addressable (~> 2.3)
+ autoparse (~> 0.3)
+ extlib (~> 0.9)
+ faraday (~> 0.9)
+ googleauth (~> 0.3)
+ launchy (~> 2.4)
+ multi_json (~> 1.10)
+ retriable (~> 1.4)
+ signet (~> 0.6)
+ autoparse (0.3.3)
+ addressable (>= 2.3.1)
+ extlib (>= 0.9.15)
+ multi_json (>= 1.0.0)
+ concurrent-ruby (1.1.5)
+ extlib (0.9.16)
+ faraday (0.15.4)
+ multipart-post (>= 1.2, < 3)
+ googleauth (0.8.1)
+ faraday (~> 0.12)
+ jwt (>= 1.4, < 3.0)
+ memoist (~> 0.16)
+ multi_json (~> 1.11)
+ os (>= 0.9, < 2.0)
+ signet (~> 0.7)
+ i18n (0.9.5)
+ concurrent-ruby (~> 1.0)
+ json (2.2.0)
+ jwt (1.5.6)
+ launchy (2.4.3)
+ addressable (~> 2.3)
+ memoist (0.16.0)
+ metaclass (0.0.4)
+ minitest (5.11.3)
+ mocha (1.8.0)
+ metaclass (~> 0.0.1)
+ multi_json (1.13.1)
+ multipart-post (2.1.1)
+ os (1.0.1)
+ public_suffix (3.0.3)
+ rake (12.3.2)
+ retriable (1.4.1)
+ signet (0.11.0)
+ addressable (~> 2.3)
+ faraday (~> 0.9)
+ jwt (>= 1.5, < 3.0)
+ multi_json (~> 1.10)
+ thread_safe (0.3.6)
+ tzinfo (1.2.5)
+ thread_safe (~> 0.1)
+
+PLATFORMS
+ ruby
+
+DEPENDENCIES
+ arvados-login-sync!
+ minitest (>= 5.0.0)
+ mocha (>= 1.5.0)
+ rake
+
+BUNDLED WITH
+ 1.17.3
projects / arvados.git / commitdiff